Role of BrSDG8 on bolting in Chinese cabbage (Brassica rapa).
Abstract KEY MESSAGE: Mapping and resequencing of two allelic early bolting mutants ebm5-1 and ebm5-2 revealed that the BrSDG8 gene is related to bolting in Chinese cabbage (Brassica rapa ssp. pekinensis). Bolting influences the leafy head formation and seed yield of Chinese cabbage therefore being an important agronomic trait. Herein, two allelic early bolting mutants, ebm5-1 and ebm5-2, stably inherited in Chinese cabbage were obtained from wild-type 'FT' seeds by ethyl methane sulfonate mutagenesis. Both mutants flowered significantly earlier than 'FT,' and genetic analysis revealed that the early bolting of th...
Source: TAG. Theoretical and Applied Genetics - July 12, 2020 Category: Genetics & Stem Cells Authors: Fu W, Huang S, Gao Y, Zhang M, Qu G, Wang N, Liu Z, Feng H Tags: Theor Appl Genet Source Type: research

The impact of the indica rice SSIIa allele on the apparent high amylose starch from rice grain with downregulated japonica SBEIIb.
Abstract KEY MESSAGE: Catalytically active indica SSIIa allele in high amylose rice with down-regulated japonica SBEIIb can increase starch content and modify the starch structure and properties without changing its amylose content. Rice (Oryza sativa) genotypes with inactive starch synthase IIa (SSIIa) with recessive variants of starch branching enzyme IIb (SBEIIb) exhibit a range of alterations in grain phenotype, starch granule morphology, starch granule bound proteins, starch structure, and functional properties. However, the interactions between the two enzymes have not been thoroughly investigated yet. We an...
Source: TAG. Theoretical and Applied Genetics - July 10, 2020 Category: Genetics & Stem Cells Authors: Luo J, Butardo VM, Yang Q, Konik-Rose C, Colgrave ML, Millar A, Jobling SA, Li Z Tags: Theor Appl Genet Source Type: research

The Hessian fly recessive resistance gene h4 mapped to chromosome 1A of the wheat cultivar 'Java' using genotyping-by-sequencing.
Abstract KEY MESSAGE: The recessive Hessian fly resistance gene h4 and flanking SNP markers were located to a 642 kb region in chromosome 1A of the wheat cultivar 'Java.' Hessian fly (HF), Mayetiola destructor, is one of the most destructive insect pests in wheat worldwide. The wheat cultivar 'Java' was reported to carry a recessive gene (h4) for HF resistance; however, its chromosome location has not been determined. To map the HF resistance gene in Java, two populations of recombinant inbred lines (RILs) were developed from 'Bobwhite' × Java and 'Overley' × Java, resp...
Source: TAG. Theoretical and Applied Genetics - July 2, 2020 Category: Genetics & Stem Cells Authors: Niu F, Xu Y, Liu X, Zhao L, Bernardo A, Li Y, Liu G, Chen MS, Cao L, Hu Z, Xu X, Bai G Tags: Theor Appl Genet Source Type: research

Effect of germination potential on storage lipids and transcriptome changes in premature developing seeds of oilseed rape (Brassica napus L.).
Abstract KEY MESSAGE: We provided a gene pool of moderate size for selecting or manipulating the candidate genes that favour the acquisition of seed dormancy, shedding light on the elevation of seed oil content in oilseed rape by blocking lipid degradation in developing seeds. In oilseed rape, the association between the germination potential of premature seeds and the final level of seed lipids, and the underlying mechanism, is elusive. Here, we investigated phenotypic differences in the germination percentage of premature seeds in a collection of oilseed rape cultivars. We compared the dynamic lipid accumulation...
Source: TAG. Theoretical and Applied Genetics - July 2, 2020 Category: Genetics & Stem Cells Authors: Zhu L, Zhao X, Xu Y, Wang Q, Wang H, Wu D, Jiang L Tags: Theor Appl Genet Source Type: research

Identification and editing of a hybrid lethality gene expands the range of interspecific hybridization potential in Nicotiana.
Abstract KEY MESSAGE: Identification and inactivation of hybrid lethality genes can be used to expand the available gene pool for improvement of a cultivated crop species. Hybrid lethality is one genetic mechanism that contributes to reproductive isolation in plants and serves as a barrier to use of diverse germplasm for improvement of cultivated species. A classic example is the seedling lethality exhibited by progeny from the Nicotiana tabacum × N. africana interspecific cross. In order to increase the body of knowledge on mechanisms of hybrid lethality in plants, and to potentially develop t...
Source: TAG. Theoretical and Applied Genetics - July 1, 2020 Category: Genetics & Stem Cells Authors: Ma J, Hancock WG, Nifong JM, Kernodle SP, Lewis RS Tags: Theor Appl Genet Source Type: research

Creation of fertility-restored materials for Ogura CMS in Brassica oleracea by introducing Rfo gene from Brassica napus via an allotriploid strategy.
In this study, the triploid strategy was used with the aim to create euploid B. oleracea progenies with the Rfo gene. The allotriploid AAC hybrid YL2 was used as a male parent to backcross with Ogura CMS Chinese kale. After successive backcrosses, the BC2Rfo-positive individual 16CMSF2-11 and its BC3 progenies, with 18 chromosomes, were developed, which were morphologically identical to the parent Chinese kale. Compared with F1 and BC1 plants, it showed stable fertility performance, and regular meiosis behavior and could produce seeds normally under natural pollination. The genomic composition analysis of Rfo-positive prog...
Source: TAG. Theoretical and Applied Genetics - July 1, 2020 Category: Genetics & Stem Cells Authors: Yu HL, Li ZY, Ren WJ, Han FQ, Yang LM, Zhuang M, Lv HH, Liu YM, Fang ZY, Zhang YY Tags: Theor Appl Genet Source Type: research

Temporal covariance structure of multi-spectral phenotypes and their predictive ability for end-of-season traits in maize.
Abstract KEY MESSAGE: Heritable variation in phenotypes extracted from multi-spectral images (MSIs) and strong genetic correlations with end-of-season traits indicates the value of MSIs for crop improvement and modeling of plant growth curve. Vegetation indices (VIs) derived from multi-spectral imaging (MSI) platforms can be used to study properties of crop canopy, providing non-destructive phenotypes that could be used to better understand growth curves throughout the growing season. To investigate the amount of variation present in several VIs and their relationship with important end-of-season traits, genetic a...
Source: TAG. Theoretical and Applied Genetics - July 1, 2020 Category: Genetics & Stem Cells Authors: Anche MT, Kaczmar NS, Morales N, Clohessy JW, Ilut DC, Gore MA, Robbins KR Tags: Theor Appl Genet Source Type: research

Genomic prediction across years in a maize doubled haploid breeding program to accelerate early-stage testcross testing.
P, Zhang X Abstract KEY MESSAGE: Genomic selection with a multiple-year training population dataset could accelerate early-stage testcross testing by skipping the first-stage yield testing, which significantly saves the time and cost of early-stage testcross testing. With the development of doubled haploid (DH) technology, the main task for a maize breeder is to estimate the breeding values of thousands of DH lines annually. In early-stage testcross testing, genomic selection (GS) offers the opportunity of replacing expensive multiple-environment phenotyping and phenotypic selection with lower-cost genotyping and...
Source: TAG. Theoretical and Applied Genetics - June 30, 2020 Category: Genetics & Stem Cells Authors: Wang N, Wang H, Zhang A, Liu Y, Yu D, Hao Z, Ilut D, Glaubitz JC, Gao Y, Jones E, Olsen M, Li X, San Vicente F, Prasanna BM, Crossa J, Pérez-Rodríguez P, Zhang X Tags: Theor Appl Genet Source Type: research

Genome-wide association analysis of stem water-soluble carbohydrate content in bread wheat.
This study provided a genome-wide landscape of the genetic architecture of SWSCC, gave a perspective for understanding the relationship between WSC and GY and explored the theoretical basis for co-improvement of WSC and GY. It also provided valuable loci and markers for future breeding. PMID: 32594265 [PubMed - as supplied by publisher] (Source: TAG. Theoretical and Applied Genetics)
Source: TAG. Theoretical and Applied Genetics - June 27, 2020 Category: Genetics & Stem Cells Authors: Fu L, Wu J, Yang S, Jin Y, Liu J, Yang M, Rasheed A, Zhang Y, Xia X, Jing R, He Z, Xiao Y Tags: Theor Appl Genet Source Type: research

A combination of linkage mapping and GWAS brings new elements on the genetic basis of yield-related traits in maize across multiple environments.
This study used an inter-mated B73 × Mo17 (IBM) Syn10 doubled-haploid (DH) population and an association panel to identify the genetic loci responsible for nine yield-related traits in maize. Using quantitative trait loci (QTL) mapping, 100 QTL influencing these traits were detected across different environments in the IBM Syn10 DH population, with 25 co-detected in multiple environments. Using a genome-wide association study (GWAS), 138 single-nucleotide polymorphisms (SNPs) were identified as correlated with these traits (P 
Source: TAG. Theoretical and Applied Genetics - June 27, 2020 Category: Genetics & Stem Cells Authors: Zhang X, Guan Z, Li Z, Liu P, Ma L, Zhang Y, Pan L, He S, Zhang Y, Li P, Ge F, Zou C, He Y, Gao S, Pan G, Shen Y Tags: Theor Appl Genet Source Type: research

Expectation and variance of the estimator of the maximized selection response of linear selection indices with normal distribution.
ssa J Abstract KEY MESSAGE: The expectation and variance of the estimator of the maximized index selection response allow the breeders to construct confidence intervals and to complete the analysis of a selection process. The maximized selection response and the correlation of the linear selection index (LSI) with the net genetic merit are the main criterion to compare the efficiency of any LSI. The estimator of the maximized selection response is the square root of the variance of the estimated LSI values multiplied by the selection intensity. The expectation and variance of this estimator allow the breeder to co...
Source: TAG. Theoretical and Applied Genetics - June 20, 2020 Category: Genetics & Stem Cells Authors: Cerón-Rojas JJ, Crossa J Tags: Theor Appl Genet Source Type: research

Fine mapping of the Ca3GT gene controlling anthocyanin biosynthesis in mature unripe fruit of Capsicum annuum L.
Abstract KEY MESSAGE: The anthocyanin biosynthesis gene Ca3GT was fine-mapped in a 110.5-kb region through a map-based cloning strategy. Gene expression and promoter analyses confirmed the strong candidate gene Capana10g001978. Pepper (Capsicum annum L.) fruit can be dark green, green, light green, purple, yellow, or ivory at the juvenile stage. Anthocyanins are responsible for fruit color formation in mature unripe pepper fruit, and transient accumulation of anthocyanins is the main problem in breeding pepper plants with mature purple fruit. Only a few genes controlling this trait have been cloned. The present st...
Source: TAG. Theoretical and Applied Genetics - June 20, 2020 Category: Genetics & Stem Cells Authors: Liu J, Ai X, Wang Y, Lu Q, Li T, Wu L, Sun L, Shen H Tags: Theor Appl Genet Source Type: research

Genetic analyses of native Fusarium head blight resistance in two spring wheat populations identifies QTL near the B1, Ppd-D1, Rht-1, Vrn-1, Fhb1, Fhb2, and Fhb5 loci.
Cartney CA Abstract KEY MESSAGE: QTL analyses of two bi-parental mapping populations with AC Barrie as a parent revealed numerous FHB-resistance QTL unique to each population and uncovered novel variation near Fhb1. Fusarium head blight (FHB) is a destructive disease of wheat worldwide, leading to severe yield and quality losses. The genetic basis of native FHB resistance was examined in two populations: a recombinant inbred line population from the cross Cutler/AC Barrie and a doubled haploid (DH) population from the cross AC Barrie/Reeder. Numerous QTL were detected among the two mapping populations with many be...
Source: TAG. Theoretical and Applied Genetics - June 17, 2020 Category: Genetics & Stem Cells Authors: Thambugala D, Brûlé-Babel AL, Blackwell BA, Fedak G, Foster AJ, MacEachern D, Gilbert J, Henriquez MA, Martin RA, McCallum BD, Spaner D, Iqbal M, Pozniak CJ, N'Diaye A, McCartney CA Tags: Theor Appl Genet Source Type: research

Synergistic mutations of two rapeseed AHAS genes confer high resistance to sulfonylurea herbicides for weed control.
In this study, we developed a rapeseed line (PN19) with sulfonylurea herbicide resistance through seed mutagenesis. Molecular analysis revealed a Trp-574-Leu mutation in BnAHAS1-2R of PN19 according to the sequence of Arabidopsis thaliana, and an allele-specific cleaved amplified polymorphic sequence marker was developed to target the point mutation. A double mutant (5N) with very high sulfonylurea resistance was then created through pyramiding two mutant genes of PN19 and M342 by molecular marker-assisted selection. Herbicide resistance identification, toxicology testing, and an in vitro enzyme activity assay of AHAS in 5...
Source: TAG. Theoretical and Applied Genetics - June 15, 2020 Category: Genetics & Stem Cells Authors: Guo Y, Cheng L, Long W, Gao J, Zhang J, Chen S, Pu H, Hu M Tags: Theor Appl Genet Source Type: research

Identification of a genomic region controlling thermotolerance at flowering in maize using a combination of whole genomic re-sequencing and bulked segregant analysis.
Abstract KEY MESSAGE: A novel genomic region controlling thermotolerance at flowering was identified by the combination of whole genomic re-sequencing and bulked segregant analysis in maize. The increasing frequency of extreme high temperature has brought a great threat to the development of maize throughout its life cycle, especially during the flowering phase. However, the genetic basis of thermotolerance at flowering in maize remains poorly understood. Here, we characterized a thermotolerant maize ecotype Abe2 and dissected its genetic basis using a F2:8 recombinant inbred line (RIL) population generated from a...
Source: TAG. Theoretical and Applied Genetics - June 13, 2020 Category: Genetics & Stem Cells Authors: Zeng W, Shi J, Qiu C, Wang Y, Rehman S, Yu S, Huang S, He C, Wang W, Chen H, Chen C, Wang C, Tao Z, Li P Tags: Theor Appl Genet Source Type: research

Identification and validation of QTL for spike fertile floret and fruiting efficiencies in hexaploid wheat (Triticum aestivum L.).
This study identified and validated two QTL associated with spike fertile floret and fruiting efficiencies. They represent two new loci to use in MAS to improve wheat yield potential. The spike fruiting efficiency (FE-grains per unit spike dry weight at anthesis, GN/SDW) is a promising trait to improve wheat yield potential. It depends on fertile floret efficiency (fertile florets per unit SDW-FFE, FF/SDW) and grain set (grains per fertile floret-GST). Given its difficult measurement, it is often estimated as the grains per unit of nongrain spike dry weight at maturity (FEm). In this study, quantitative trait loci (QTL) we...
Source: TAG. Theoretical and Applied Genetics - June 9, 2020 Category: Genetics & Stem Cells Authors: Pretini N, Vanzetti LS, Terrile II, Börner A, Plieske J, Ganal M, Röder M, González FG Tags: Theor Appl Genet Source Type: research

Multi-parent multi-environment QTL analysis: an illustration with the EU-NAM Flint population.
Abstract KEY MESSAGE: Multi-parent populations multi-environment QTL experiments data should be analysed jointly to estimate the QTL effect variation within the population and between environments. Commonly, QTL detection in multi-parent populations (MPPs) data measured in multiple environments (ME) is done by analyzing genotypic values 'averaged' across environments. This method ignores the environment-specific QTL (QTLxE) effects. Running separate single environment analyses is a possibility to measure QTLxE effects, but those analyses do not model the genetic covariance due to the use of the same genotype in di...
Source: TAG. Theoretical and Applied Genetics - June 9, 2020 Category: Genetics & Stem Cells Authors: Garin V, Malosetti M, van Eeuwijk F Tags: Theor Appl Genet Source Type: research

The origin and widespread occurrence of Sli-based self-compatibility in potato.
Abstract Self-compatible (SC) diploid potatoes allow innovative potato breeding. Therefore, the Sli gene, originally described in S. chacoense, has received much attention. In elite S. tuberosum diploids, spontaneous berry set is occasionally observed. We aimed to map SC from S. tuberosum origin. Two full-sib mapping populations from non-inbred diploids were used. Bulks were composed based on both pollen tube growth and berry set upon selfing. After DNA sequencing of the parents and bulks, we generated k-mer tables. Set algebra and depth filtering were used to identify bulk-specific k-mers. Coupling and repulsion ...
Source: TAG. Theoretical and Applied Genetics - June 8, 2020 Category: Genetics & Stem Cells Authors: Clot CR, Polzer C, Prodhomme C, Schuit C, Engelen CJM, Hutten RCB, van Eck HJ Tags: Theor Appl Genet Source Type: research

A novel leaf rust resistance gene introgressed from Aegilops markgrafii maps on chromosome arm 2AS of wheat.
Abstract KEY MESSAGE: A novel leaf rust resistance gene, LrM, introgressed from Aegilops markgrafii and mapped on chromosome 2AS using SSR- and SNP-based PCR markers will aid in broadening the genetic base of rust resistance in wheat. A new leaf rust resistance gene tentatively named LrM was introgressed from the diploid non-progenitor species Ae. markgrafii (2n = 2x = 14, genome CC) into common wheat using the nulli-5B mechanism. The introgression line ER9-700 showed a high degree of resistance against a wide spectrum of Puccinia triticina pathotypes. Genetic analysis was performed usi...
Source: TAG. Theoretical and Applied Genetics - June 7, 2020 Category: Genetics & Stem Cells Authors: Rani K, Raghu BR, Jha SK, Agarwal P, Mallick N, Niranjana M, Sharma JB, Singh AK, Sharma NK, Rajkumar S, Tomar SMS, Vinod Tags: Theor Appl Genet Source Type: research

Association mapping of malting quality traits in UK spring and winter barley cultivar collections.
Abstract KEY MESSAGE: Historical malting quality data was collated from UK national and recommended list trial data and used in a GWAS. 25 QTL were identified, with the majority from spring barley cultivar sets. In Europe, the most economically significant use of barley is the production of malt for use in the brewing and distilling industries. As such, selection for traits related to malting quality is of great commercial interest. In order to study the genetic basis of variation for malting quality traits in UK cultivars, a historical set of trial data was collated from national and recommended list trials from ...
Source: TAG. Theoretical and Applied Genetics - June 6, 2020 Category: Genetics & Stem Cells Authors: Looseley ME, Ramsay L, Bull H, Swanston JS, Shaw PD, Macaulay M, Booth A, Russell JR, Waugh R, IMPROMALT Consortium, Thomas WTB Tags: Theor Appl Genet Source Type: research

Genome-wide association reveals a complex architecture for rust resistance in 2300 worldwide bread wheat accessions screened under various Australian conditions.
Abstract We utilized 2300 wheat accessions including worldwide landraces, cultivars and primary synthetic-derived germplasm with three Australian cultivars: Annuello, Yitpi and Correll, to investigate field-based resistance to leaf (Lr) rust, stem (Sr) rust and stripe (Yr) rust diseases across a range of Australian wheat agri-production zones. Generally, the resistance in the modern Australian cultivars, synthetic derivatives, South and North American materials outperformed other geographical subpopulations. Different environments for each trait showed significant correlations, with average r values of 0.53, 0.23 ...
Source: TAG. Theoretical and Applied Genetics - June 5, 2020 Category: Genetics & Stem Cells Authors: Joukhadar R, Hollaway G, Shi F, Kant S, Forrest K, Wong D, Petkowski J, Pasam R, Tibbits J, Bariana H, Bansal U, Spangenberg G, Daetwyler H, Gendall T, Hayden M Tags: Theor Appl Genet Source Type: research

Overcoming polyploidy pitfalls: a user guide for effective SNP conversion into KASP markers in wheat.
Abstract KEY MESSAGE: Conversion of SNP chip assays into locus-specific KASP markers requires adapted strategies in polyploid species with high genome homeology. Procedures are exemplified by QTL-associated SNPs in hexaploid wheat. Kompetitive allele-specific PCR (KASP) markers are commonly used in marker-assisted commercial plant breeding due to their cost-effectiveness and throughput for high sample volumes. However, conversion of trait-linked SNP markers from array-based SNP detection technologies into KASP markers is particularly challenging in polyploid crop species, due to the presence of highly similar home...
Source: TAG. Theoretical and Applied Genetics - June 4, 2020 Category: Genetics & Stem Cells Authors: Makhoul M, Rambla C, Voss-Fels KP, Hickey LT, Snowdon RJ, Obermeier C Tags: Theor Appl Genet Source Type: research

Introgression of perennial growth habit from Lophopyrum elongatum into wheat.
Abstract KEY MESSAGE: A locus for perennial growth was mapped on Lophopyrum elongatum chromosome arm 4ES and introgressed into the wheat genome. Evidence was obtained that in addition to chromosome 4E, other L. elongatum chromosomes control perennial growth. Monocarpy versus polycarpy is one of the fundamental developmental dichotomies in flowering plants. Advances in the understanding of the genetic basis of this dichotomy are important for basic biological reasons and practically for genetic manipulation of growth development in economically important plants. Nine wheat introgression lines (ILs) harboring germpl...
Source: TAG. Theoretical and Applied Genetics - June 3, 2020 Category: Genetics & Stem Cells Authors: Abbasi J, Xu J, Dehghani H, Luo MC, Deal KR, McGuire PE, Dvorak J Tags: Theor Appl Genet Source Type: research

Dissection and validation of a QTL cluster linked to Rht-B1 locus controlling grain weight in common wheat (Triticum aestivum L.) using near-isogenic lines.
This study dissected and validated a QTL cluster associated with thousand grain weight on chromosome 4B using multiple near-isogenic lines in common wheat. Grain size and weight are crucial components of wheat yield. Previously, we identified a QTL cluster for thousand grain weight (TGW) on chromosome 4B using the Nongda3338 (ND3338)/Jingdong6 (JD6) doubled haploid population. Here, near-isogenic lines (NILs) in the ND3338 background were developed to dissect and validate the QTL cluster. Based on six independent BC3F3:4 heterogeneous inbred families, the 4B QTL cluster was divided into two linked QTL intervals (designated...
Source: TAG. Theoretical and Applied Genetics - June 2, 2020 Category: Genetics & Stem Cells Authors: Guan P, Shen X, Mu Q, Wang Y, Wang X, Chen Y, Zhao Y, Chen X, Zhao A, Mao W, Guo Y, Xin M, Hu Z, Yao Y, Ni Z, Sun Q, Peng H Tags: Theor Appl Genet Source Type: research

QTL mapping for field resistance to wheat blast in the Caninde#1/Alondra population.
Abstract KEY MESSAGE: Wheat blast resistance in Caninde#1 is controlled by a major QTL on 2NS/2AS translocation and multiple minor QTL in an additive mode. Wheat blast (WB) is a devastating disease in South America, and it recently also emerged in Bangladesh. Host resistance to WB has relied heavily on the 2NS/2AS translocation, but the responsible QTL has not been mapped and its phenotypic effects in different environments have not been reported. In the current study, a recombinant inbred line population with 298 progenies was generated, with the female and male parents being Caninde#1 (with 2NS) and Alondra (wit...
Source: TAG. Theoretical and Applied Genetics - June 2, 2020 Category: Genetics & Stem Cells Authors: He X, Kabir MR, Roy KK, Anwar MB, Xu K, Marza F, Odilbekov F, Chawade A, Duveiller E, Huttner E, Singh PK Tags: Theor Appl Genet Source Type: research

Whole-genome sequencing reveals uniqueness of black-hulled and straw-hulled weedy rice genomes.
Abstract KEY MESSAGE: Both SH and BHA weedy rice genotypes evolved independently and have distinct genomic composition. Different genetic mechanisms may be responsible for their competitiveness and adaptation to diverse environmental conditions. Two major types of weedy rice are recognized in the USA based on morphology: straw-hull (SH) and black-hull awned (BHA) weedy rice. We performed whole-genome resequencing of a SH weedy rice 'PSRR-1', a BHA weedy rice 'BHA1115', and a japonica cultivar 'Cypress' to delineate genome-wide differences and their relevance to genetics and evolution of weedy attributes. The high-...
Source: TAG. Theoretical and Applied Genetics - June 2, 2020 Category: Genetics & Stem Cells Authors: Islam MS, Coronejo S, Subudhi PK Tags: Theor Appl Genet Source Type: research

The value of early-stage phenotyping for wheat breeding in the age of genomic selection.
Abstract KEY MESSAGE: Genomic selection using data from an on-going breeding program can improve gain from selection, relative to phenotypic selection, by significantly increasing the number of lines that can be evaluated. The early stages of phenotyping involve few observations and can be quite inaccurate. Genomic selection (GS) could improve selection accuracy and alter resource allocation. Our objectives were (1) to compare the prediction accuracy of GS and phenotyping in stage-1 and stage-2 field evaluations and (2) to assess the value of stage-1 phenotyping for advancing lines to stage-2 testing. We built tra...
Source: TAG. Theoretical and Applied Genetics - June 1, 2020 Category: Genetics & Stem Cells Authors: Borrenpohl D, Huang M, Olson E, Sneller C Tags: Theor Appl Genet Source Type: research

Mapping Solanum chacoense mediated Colorado potato beetle (Leptinotarsa decemlineata) resistance in a self-compatible F2 diploid population.
We examined the genetic features underlying leptine glycoalkaloid mediated Colorado potato beetle (Leptinotarsa decemlineata) host plant resistance in a diploid F2 mapping population of 233 individuals derived from Solanum chacoense lines USDA8380-1 and M6. The presence of foliar leptine glycoalkaloids in this population segregated as a single dominant gene and displayed continuous distribution of accumulated quantity in those individuals producing the compound. Using biparental linkage mapping, a major overlapping QTL region with partial dominance effects was identified on chromosome 2 explaining 49.3% and 34.1% of the va...
Source: TAG. Theoretical and Applied Genetics - May 30, 2020 Category: Genetics & Stem Cells Authors: Kaiser N, Manrique-Carpintero NC, DiFonzo C, Coombs J, Douches D Tags: Theor Appl Genet Source Type: research

A minor QTL, SG3, encoding an R2R3-MYB protein, negatively controls grain length in rice.
In this study, we focused on the isolation of a minor grain length QTL, small grain 3 (SG3), which is closely linked to the major QTL grain size 3 (GS3). The genetic effect of SG3 on grain length was dependent on GS3 status. Its genetic effect was larger in the presence of nonfunctional sg3 than functional SG3. A large number of near-isogenic F2 plants in which GS3 was fixed with nonfunctional alleles were developed to clone SG3. A gene encoding an R2R3 MYB domain transcriptional regulator was identified as the candidate gene for SG3. SG3 overexpression and knockdown plants showed shortened and elongated grains, respective...
Source: TAG. Theoretical and Applied Genetics - May 29, 2020 Category: Genetics & Stem Cells Authors: Li Q, Lu L, Liu H, Bai X, Zhou X, Wu B, Yuan M, Yang L, Xing Y Tags: Theor Appl Genet Source Type: research

Genetic mapping of quantitative trait loci and a major locus for resistance to grey leaf spot in maize.
Abstract KEY MESSAGE: The genetic basis of GLS resistance was dissected using two DH populations sharing a common resistant parent. A major QTL repeatedly detected in multiple developmental stages and environments was fine mapped in a backcross population. Grey leaf spot (GLS), caused by Cercospora zeae-maydis or Cercospora zeina, is a highly destructive foliar disease worldwide. However, the mechanism of resistance against GLS is not well understood. To study the inheritance of this resistance, we developed two doubled haploid (DH) populations sharing a common resistant parent. The two DH populations were grown i...
Source: TAG. Theoretical and Applied Genetics - May 28, 2020 Category: Genetics & Stem Cells Authors: Du L, Yu F, Zhang H, Wang B, Ma K, Yu C, Xin W, Huang X, Liu Y, Liu K Tags: Theor Appl Genet Source Type: research

Strategies for eQTL mapping in allopolyploid organisms.
This study uses simulations to explore statistical power and false-positive rates for eQTL mapping in allopolyploid organisms and provides guidelines to apply eQTL mapping in these organisms. In recent years, RNA-seq has become the dominant technology for eQTL studies. However, most work has been in diploid organisms. Many species of economic and environmental importance are polyploid, and approaches for eQTL mapping in polyploids are not well developed. High similarity between duplicated genes in polyploids will cause misassignment of sequence reads and may cause false-positive results and/or lack of power to detect eQTL....
Source: TAG. Theoretical and Applied Genetics - May 27, 2020 Category: Genetics & Stem Cells Authors: Fan KH, Devos KM, Schliekelman P Tags: Theor Appl Genet Source Type: research

Dominant complementary interaction between OsC1 and two tightly linked genes, Rb1 and Rb2, controls the purple leaf sheath in rice.
Abstract KEY MESSAGE: Two tightly linked genes for rice purple leaf sheath were identified via map-based cloning. Further analysis indicated that these two genes together with OsC1 co-regulating the purple leaf sheath. The purple color of the leaf sheath in rice is dependent on the accumulation of anthocyanins such as cyanidin 3-O-glucoside (C3G) and peonidin 3-O-glucoside (P3G). Although many genes related to leaf sheath color have been mapped, the genetic basis for leaf sheath color is not yet clear. Here, PSH1 (purple leaf sheath 1) was mapped to chromosome 1 using an F2 and a RIL population. Map-based cloning ...
Source: TAG. Theoretical and Applied Genetics - May 26, 2020 Category: Genetics & Stem Cells Authors: Hu W, Zhou T, Han Z, Tan C, Xing Y Tags: Theor Appl Genet Source Type: research

Development and validation of high-throughput and low-cost STARP assays for genes underpinning economically important traits in wheat.
In this study, we developed 56 gene-specific semi-thermal asymmetric reverse PCR (STARP) markers for wheat quality, tolerance to biotic and abiotic stresses, grain yield, and adaptation-related traits. The STARP assays were validated by (1) comparison of the assays with corresponding diagnostic STS/CAPS markers on 40 diverse wheat cultivars and (2) characterization of allelic effects based on the phenotypic and genotypic data of three segregating populations and 305 diverse wheat accessions from China and 13 other countries. The STARP assays showed the advantages of high-throughput, accuracy, flexibility, simple assay desi...
Source: TAG. Theoretical and Applied Genetics - May 25, 2020 Category: Genetics & Stem Cells Authors: Wu Y, Li M, He Z, Dreisigacker S, Wen W, Jin H, Zhai S, Li F, Gao F, Liu J, Wang R, Zhang P, Wan Y, Cao S, Xia X Tags: Theor Appl Genet Source Type: research

Identification and fine mapping of spot blotch (Bipolaris sorokiniana) resistance gene Sb4 in wheat.
This study provides a foundational step for further cloning of Sb4 using a map-based approach. PMID: 32451599 [PubMed - as supplied by publisher] (Source: TAG. Theoretical and Applied Genetics)
Source: TAG. Theoretical and Applied Genetics - May 25, 2020 Category: Genetics & Stem Cells Authors: Zhang P, Guo G, Wu Q, Chen Y, Xie J, Lu P, Li B, Dong L, Li M, Wang R, Yuan C, Zhang H, Zhu K, Li W, Liu Z Tags: Theor Appl Genet Source Type: research

Modifications of fatty acid profile through targeted mutation at BnaFAD2 gene with CRISPR/Cas9-mediated gene editing in Brassica napus.
In this study, we further established spatiotemporal expression pattern of each copy of BnaFAD2 using published RNA-seq data. Genomic editing technology based on CRISPR/Cas9 system was used to mutate all the copies of BnaFAD2 to create novel allelic variations in oleic acid and other fatty acid levels. A number of mutants at two targeting sites were identified, and the phenotypic variation in the mutants was systematically evaluated. The oleic acid content in the seed of the mutants increased significantly with the highest exceeding 80% compared with wild type of 66.43%, while linoleic and linolenic acid contents decreased...
Source: TAG. Theoretical and Applied Genetics - May 24, 2020 Category: Genetics & Stem Cells Authors: Huang H, Cui T, Zhang L, Yang Q, Yang Y, Xie K, Fan C, Zhou Y Tags: Theor Appl Genet Source Type: research

Identifying barley pan-genome sequence anchors using genetic mapping and machine learning.
Abstract KEY MESSAGE: We identified 1.844 million barley pan-genome sequence anchors from 12,306 genotypes using genetic mapping and machine learning. There is increasing evidence that genes from a given crop genotype are far to cover all genes in that species; thus, building more comprehensive pan-genomes is of great importance in genetic research and breeding. Obtaining a thousand-genotype scale pan-genome using deep-sequencing data is currently impractical for species like barley which has a huge and highly repetitive genome. To this end, we attempted to identify barley pan-genome sequence anchors from a large ...
Source: TAG. Theoretical and Applied Genetics - May 24, 2020 Category: Genetics & Stem Cells Authors: Gao S, Wu J, Stiller J, Zheng Z, Zhou M, Wang YG, Liu C Tags: Theor Appl Genet Source Type: research

Transcriptomic and biochemical analyses of the accumulation of sucrose in mungbean (Vigna radiata (L.) Wilczek) leaves after pod removal.
Abstract KEY MESSAGE: Synchronous pod maturity is critical for increasing grain yield. The candidate genes involved in synchronous pod maturity were identified through RNA-seq and HPLC. Mungbean (Vigna radiata [L.] Wilczek), an important source of carbohydrate and protein in Asia, is characterized by nonsynchronous pod maturity; consequently, harvesting is labor intensive. Because pod maturity is associated with synthesis and remobilization of sucrose, we examined changes in sucrose levels and transcriptome in leaf (source) tissues after pod (sink) removal using two genotypes, VC1973A and V2984; VC1973A had higher...
Source: TAG. Theoretical and Applied Genetics - May 23, 2020 Category: Genetics & Stem Cells Authors: Ha J, Shim S, Lee T, Lee E, Yang X, Jeong H, Kim MY, Lee SH Tags: Theor Appl Genet Source Type: research

Meta-QTL analysis of tan spot resistance in wheat.
In this study, we performed a meta-QTL analysis of tan spot resistance using the reported QTL from 15 previous QTL mapping studies. An integrated linkage map with a total length of 4080.5 cM containing 47,309 markers was assembled from 21 individual linkage maps and three previously published consensus maps. Nineteen meta-QTL were clustered from 104 initial QTL projected on the integrated map. Three of the 19 meta-QTL located on chromosomes 2A, 3B, and 5A show large genetic effects and confer resistance to multiple races in multiple bread wheat and durum wheat mapping populations. The integration of those race-nonspec...
Source: TAG. Theoretical and Applied Genetics - May 20, 2020 Category: Genetics & Stem Cells Authors: Liu Y, Salsman E, Wang R, Galagedara N, Zhang Q, Fiedler JD, Liu Z, Xu S, Faris JD, Li X Tags: Theor Appl Genet Source Type: research

Identification of two novel Hessian fly resistance genes H35 and H36 in a hard winter wheat line SD06165.
Abstract KEY MESSAGE: Two new Hessian fly resistance QTLs (H35 and H36) and tightly linked SNP markers were identified in a US hard winter wheat SD06165. Hessian fly (HF), Mayetiola destructor (Say), is one of the most destructive pests in wheat (Triticum aestivum L.) worldwide. Growing resistant cultivars is the most effective approach to minimize Hessian fly damage. To identify new quantitative trait loci (QTLs) for HF resistance, a recombinant inbred line population was developed by crossing HF resistant wheat line SD06165 to a susceptible line OK05312. The population was genotyped with 1709 single-nucleotide p...
Source: TAG. Theoretical and Applied Genetics - May 20, 2020 Category: Genetics & Stem Cells Authors: Zhao L, Abdelsalam NR, Xu Y, Chen MS, Feng Y, Kong L, Bai G Tags: Theor Appl Genet Source Type: research

Identification and validation of stable quantitative trait loci for grain filling rate in common wheat (Triticum aestivum L.).
Abstract KEY MESSAGE: We identified and validated two stable grain filling rate (GFR) quantitative trait loci (QTL) in wheat that positively influenced several yield-related traits. Among them, QGfr.sicau-7D.1 was a novel GFR QTL. The grain filling rate (GFR) plays a crucial role in determining grain yield. To advance the current understanding of the genetic characteristics underlying the GFR in common wheat, three recombinant inbred line populations were used to map and validate GFR quantitative trait loci (QTL). Using a high-density genetic linkage map, 10 GFR QTL were detected. They were located on chromosomes ...
Source: TAG. Theoretical and Applied Genetics - May 19, 2020 Category: Genetics & Stem Cells Authors: Lin Y, Jiang X, Tao Y, Yang X, Wang Z, Wu F, Liu S, Li C, Deng M, Ma J, Chen G, Wei Y, Zheng Y, Liu Y Tags: Theor Appl Genet Source Type: research

Effective identification of CRISPR/Cas9-induced and naturally occurred mutations in rice using a multiplex ligation-dependent probe amplification-based method.
Abstract KEY MESSAGE: A multiplex ligation-dependent probe amplification (MLPA)-based method was developed and successfully utilized to efficiently detect both CRISPR/Cas9-induced and naturally occurred mutations in rice. The site-specific nuclease-based CRISPR/Cas9 system has emerged as one of the most efficient genome editing tools to modify multiple genomic targets simultaneously in various organisms, including plants for both fundamental and applied researches. Screening for both on-target and off-target mutations in CRISPR/Cas9-generated mutants at the early stages is an indispensable step for functional anal...
Source: TAG. Theoretical and Applied Genetics - May 14, 2020 Category: Genetics & Stem Cells Authors: Biswas S, Li R, Hong J, Zhao X, Yuan Z, Zhang D, Shi J Tags: Theor Appl Genet Source Type: research

Fine mapping QSc.VR4, an effective and stable scald resistance locus in barley (Hordeum vulgare L.), to a 0.38-Mb region enriched with LRR-RLK and GLP genes.
Abstract KEY MESSAGE: An effective and stable quantitative resistance locus, QSc.VR4, was fine mapped, characterized and physically anchored to the short arm of 4H, conferring adult plant resistance to the fungus Rhynchosporium commune in barley. Scald caused by Rhynchosporium commune is one of the most destructive barley diseases worldwide. Accumulation of adult plant resistance (APR) governed by multiple resistance alleles is predicted to be effective and long-lasting against a broad spectrum of pathotypes. However, the molecular mechanisms that control APR remain poorly understood. Here, quantitative trait loci...
Source: TAG. Theoretical and Applied Genetics - May 13, 2020 Category: Genetics & Stem Cells Authors: Wang Y, Xu Y, Gupta S, Zhou Y, Wallwork H, Zhou G, Broughton S, Zhang XQ, Tan C, Westcott S, Moody D, Sun D, Loughman R, Zhang W, Li C Tags: Theor Appl Genet Source Type: research

Speed breeding short-day crops by LED-controlled light schemes.
In this study, we present a speed breeding protocol based on light-emitting diodes (LEDs) that allow to modify light quality, and exemplarily demonstrate its effectiveness for the short-day crops soybean (Glycine max), rice (Oryza sativa) and amaranth (Amaranthus spp.). Adjusting the photoperiod to 10 h and using a blue-light enriched, far-red-deprived light spectrum facilitated the growth of short and sturdy soybean plants that flowered ~ 23 days after sowing and matured within 77 days, thus allowing up to five generations per year. In rice and amaranth, flowering was achieved ~ ...
Source: TAG. Theoretical and Applied Genetics - May 12, 2020 Category: Genetics & Stem Cells Authors: Jähne F, Hahn V, Würschum T, Leiser WL Tags: Theor Appl Genet Source Type: research

QTL analysis of cooking time and quality traits in dry bean (Phaseolus vulgaris L.).
Abstract KEY MESSAGE: Three robust QTL for dry bean cooking time shortened cooking time 11-26 min and co-localized with QTL for increased cooked seed protein concentration. Cooking time is a major factor associated with consumer preference of dry beans (Phaseolus vulgaris L.). The genetic control of cooking time was investigated with a quantitative trait loci (QTL) study on a recombinant inbred line (RIL) population developed from TZ-27 (slow cooking) and TZ-37 (fast cooking). The RIL population of 146 lines was grown on research farms over 2 years in Arusha and Morogoro, Tanzania. Arusha is an important...
Source: TAG. Theoretical and Applied Genetics - May 6, 2020 Category: Genetics & Stem Cells Authors: Berry M, Izquierdo P, Jeffery H, Shaw S, Nchimbi-Msolla S, Cichy K Tags: Theor Appl Genet Source Type: research

Characterization of a major quantitative trait locus on the short arm of chromosome 4B for spike number per unit area in common wheat (Triticum aestivum L.).
In this study, we used the F2 population derived from a cross between two wheat accessions displaying significant differences in SNPA to perform quantitative trait locus (QTL) analysis. Through bulked segregant analysis, a major and stable QTL that explained 18.11-82.11% of the phenotypic variation was identified on chromosome 4BS. The QTL interval was validated using F4:5 and F6:7 families and narrowed it to a 24.91-38.36 Mb region of chromosome 4BS according to the 'Chinese Spring' reference genome sequence. In this region, variations in 16 genes caused amino acid changes and three genes were present in only one par...
Source: TAG. Theoretical and Applied Genetics - April 28, 2020 Category: Genetics & Stem Cells Authors: Li J, Wen S, Fan C, Zhang M, Tian S, Kang W, Zhao W, Bi C, Wang Q, Lu S, Guo W, Ni Z, Xie C, Sun Q, You M Tags: Theor Appl Genet Source Type: research

Translational genomics for achieving higher genetic gains in groundnut.
Abstract KEY MESSAGE: Groundnut has entered now in post-genome era enriched with optimum genomic and genetic resources to facilitate faster trait dissection, gene discovery and accelerated genetic improvement for developing climate-smart varieties. Cultivated groundnut or peanut (Arachis hypogaea), an allopolyploid oilseed crop with a large and complex genome, is one of the most nutritious food. This crop is grown in more than 100 countries, and the low productivity has remained the biggest challenge in the semiarid tropics. Recently, the groundnut research community has witnessed fast progress and achieved severa...
Source: TAG. Theoretical and Applied Genetics - April 23, 2020 Category: Genetics & Stem Cells Authors: Pandey MK, Pandey AK, Kumar R, Nwosu CV, Guo B, Wright GC, Bhat RS, Chen X, Bera SK, Yuan M, Jiang H, Faye I, Radhakrishnan T, Wang X, Liang X, Liao B, Zhang X, Varshney RK, Zhuang W Tags: Theor Appl Genet Source Type: research

Exploiting the genome of Thinopyrum elongatum to expand the gene pool of hexaploid wheat.
Abstract KEY MESSAGE: One hundred and thirty four introgressions from Thinopyrum elongatum have been transferred into a wheat background and were characterised using 263 SNP markers. Species within the genus Thinopyrum have been shown to carry genetic variation for a very wide range of traits including biotic and abiotic stresses and quality. Research has shown that one of the species within this genus, Th. elongatum, has a close relationship with the genomes of wheat making it a highly suitable candidate to expand the gene pool of wheat. Homoeologous recombination, in the absence of the Ph1 gene, has been exploit...
Source: TAG. Theoretical and Applied Genetics - April 20, 2020 Category: Genetics & Stem Cells Authors: Baker L, Grewal S, Yang CY, Hubbart-Edwards S, Scholefield D, Ashling S, Burridge AJ, Przewieslik-Allen AM, Wilkinson PA, King IP, King J Tags: Theor Appl Genet Source Type: research

QTL for horticulturally important traits associated with pleiotropic andromonoecy and carpel number loci, and a paracentric inversion in cucumber.
In this study, we conducted QTL mapping using F2 and recombinant inbred line (RIL) populations from the WI2757 × True Lemon cross that were segregating for multiple traits. Phenotypic data were collected in replicated field trials across multiple years for seven traits including fruit carpel number (CN) and sex expression. A high-density SNP-based genetic map was developed with genotyping by sequencing of the RIL population, which revealed a region on chromosome 1 with strong recombination suppression. The reduced recombination in this region was due to a ~ 10-Mbp paracentric inversion in ...
Source: TAG. Theoretical and Applied Genetics - April 18, 2020 Category: Genetics & Stem Cells Authors: Pan Y, Wen C, Han Y, Wang Y, Li Y, Li S, Cheng X, Weng Y Tags: Theor Appl Genet Source Type: research

Crop genetics research in Asia: improving food security and nutrition.
PMID: 32306095 [PubMed - as supplied by publisher] (Source: TAG. Theoretical and Applied Genetics)
Source: TAG. Theoretical and Applied Genetics - April 18, 2020 Category: Genetics & Stem Cells Authors: Zhang Q, Xu M, Xia X, Komatsuda T, Varshney RK, Shi K Tags: Theor Appl Genet Source Type: research

Economical optimization of a breeding scheme by selective phenotyping of the calibration set in a multi-trait context: application to bread making quality.
This study compares different strategies of genomic prediction to optimize resource allocation in breeding schemes by using information from cheaper correlated traits to predict a more expensive trait of interest. We used bread wheat baking score (BMS) calculated for French registration as a case study. To conduct this project, 398 lines from a public breeding program were genotyped and phenotyped for BMS and correlated traits in 11 locations in France between 2000 and 2016. Single-trait (ST), multi-trait (MT) and trait-assisted (TA) strategies were compared in terms of predictive ability and cost. In MT and TA strategies,...
Source: TAG. Theoretical and Applied Genetics - April 17, 2020 Category: Genetics & Stem Cells Authors: Ben-Sadoun S, Rincent R, Auzanneau J, Oury FX, Rolland B, Heumez E, Ravel C, Charmet G, Bouchet S Tags: Theor Appl Genet Source Type: research